X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=416773d9035986e9b59ee92537fa3f415a616332;hb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;hp=9913428b0937f183f74d79eda02b6fcdcc06f4d5;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 9913428..416773d 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,7 +20,14 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -153,8 +160,10 @@ public class FormatAdapter extends AppletFormatAdapter
   public boolean getCacheSuffixDefault(String format)
   {
     if (isValidFormat(format))
+    {
       return jalview.bin.Cache.getDefault(format.toUpperCase()
               + "_JVSUFFIX", true);
+    }
     return false;
   }
 
@@ -226,6 +235,41 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
+  public Alignment readFile(String inFile, String type, String format)
+          throws java.io.IOException
+  {
+    Alignment al;
+    if (format.equals("HTML"))
+    {
+      afile = new HtmlFile(inFile, type);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(al);
+    }
+    else
+    {
+      al = super.readFile(inFile, type, format);
+    }
+
+    return al;
+  }
+
+  public AlignmentI readFromFile(FileParse source, String format)
+          throws java.io.IOException
+  {
+    Alignment al;
+    if (format.equals("HTML"))
+    {
+      afile = new HtmlFile(source);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(al);
+    }
+    else
+    {
+      al = (Alignment) super.readFromFile(source, format);
+    }
+    return al;
+  }
+
   /**
    * validate format is valid for IO in Application. This is basically the
    * AppletFormatAdapter.isValidFormat call with additional checks for
@@ -247,4 +291,16 @@ public class FormatAdapter extends AppletFormatAdapter
     }
     return AppletFormatAdapter.isValidFormat(format, forwriting);
   }
+
+  /**
+   * Create a flat file representation of a given view or selected region of a view
+   * @param format
+   * @param av
+   * @return String containing flat file
+   */
+  public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+  {
+    return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+  }
+
 }